The antigenic structures recognized by CD8+ cytotoxic T lymphocytes (CTL) are cell surface complexes formed by noncovalent association of class I proteins of the major histocompatibility complex (MHC) with short peptides, typically 8-9 amino acids in length. Around a thousand different peptide-MHC-I complexes are likely to exist for any particular MHC class I protein on a cell's surface at a sufficient density for effective interaction with CD8+ T cells. To understand how these peptides are selected from the enormously greater number of different peptides that can be potentially generated by proteolytic fragmentation of the 5,000-10,000 different proteins produced by a typical cell, we are engaged in characterizing the naturally occurring peptides that are recognized by CD8+ CTL in association with MHC-I proteins. Using a system in which CTL recognize normal cells from MHC-different individuals (i.e. alloreactive CTL that specifically respond to allogeneic cells), we have recently succeeded in characterizing two naturally occurring peptides that are recognized by an alloreactive CTL clone (2C) in association with the MHC-I protein Ld. The smaller peptide, an octamer, forms stable complexes with Ld, the larger peptide (16 amino acids in length) includes the entire sequence of the octamer and is probably its precursor in the cells that produce these peptides. since we have also identified the source ("parent protein") of these peptides we have in hand a unique system for exploring the biochemical pathways that lead to the formation of specific peptide-MHC-I complexes. Inasmuch as the parent protein is a ubiquitous dehydrogenase whose abundance can be measured by a simple assay, we will also explore how the generation of these peptides, their affinity for MHC I proteins, and the binding of the corresponding peptide-MHC-I complexes to T cell receptors influence the selection of thymocytes as they mature in the thymus, a process that is ultimately responsible for the capacity of mature T cells to recognize and respond specifically to an enormous variety of foreign peptide-MHC-I complexes but not to self-peptide-MHC-I complexes ("self-tolerance").